Flash carts that have updates support 99%+ of games at any given time. Usually if one flas hcart doesn't support a new game it's only a matter of days or weeks before an update to fix it is out.

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The only time I have ever really had compatibility issues is with the CycloDS in game menu/save states. Ever since switching to my DSTwo even save state issues have been rare (though the slowdown option does not work with Tetris).